Fremantle Harbour is Western Australia's largest and busiest general cargo port and an important historical site. The inner harbour handles a large volume of sea containers, vehicle imports and livestock exports, cruise shipping and naval visits, and operates 24 hours a day. It is located adjacent to the city of Fremantle, in the Perth metropolitan region.

Fremantle Harbour consists of the Inner Harbour, which is situated on the mouth of the Swan River; the Outer Harbour, which is 20 kilometres (12 mi) south at Kwinana in Cockburn Sound and handles bulk cargo ports, grain, petroleum, liquefied petroleum gas, alumina, mineral sands, fertilisers, sulphur and other bulk commodities; and Gage Roads, which is the anchorage between Rottnest Island and the mainland. The Inner Harbour includes northern and southern wharves named North Quay and Victoria Quay respectively. All of this area is managed by Fremantle Ports, a Government of Western Australia trading enterprise, under the registered business name Fremantle Ports.

The Inner Harbour is to be phased out and all shipping operations to be moved to the Outer Harbour, with the current Inner Harbour to be redeveloped, as shown in the Future of Fremantle Place and Economic Vision.

Fremantle's port role began immediately after the Swan River Colony was founded in 1829, but the entrance to the Swan River estuary was blocked by a rocky bar, which made the mouth of the river virtually impassable for seagoing vessels. The first steamship to enter the port was HMS Driver on 4 December 1845.

Fremantle shipping was served by the Long Jetty that extended into the open sea, where Bathers Beach is today. Cargo was offloaded onto the jetty and then taken down Cliff Street in Fremantle's West End. It was loaded onto barges that sailed up the river on the westerly sea breeze and back to Fremantle on easterly winds. Later it was transported by rail. Sailors disliked the Long Jetty; in 1892 Captain D. B. Shaw of the American barque Saranac described it as "terrible":

entered and fought against putting the vessel alongside jetty to discharge. It is a terrible place. No place to put a vessel. No shelter whatever. All the ships have to lay and discharge at the wharf or pay lighterage.... It is blowing a gale from the SW ... and takes all our time to hold her.... She had done considerable damage to herself.... It is certainly the worst place I or anyone else ever saw. No place to send a ship of this size.... Any man who would come or send a ship a second time is a damned ass.

British marine engineer John Coode advised John Forrest an outer harbour near Rous Head, or one that would stretch south from Arthur's Head, could be built. Coode ruled out building a port in the river mouth as he believed it would continually silt up due to lateral sand drift. In 1887 the Fremantle Chamber of Commerce pushed hard for the southern scheme to be chosen, but the colony could not raise the estimated cost of £500,000. By 1891 Forrest was examining another proposal: an offshore facility at Owen Anchorage south of Fremantle.

But by then Charles Yelverton O'Connor had been appointed the Colony's Engineer-in-Chief, and decided the best option was an inner harbour built in the mouth of the Swan River. The discovery of gold in Western Australia meant a working port was urgently needed, Parliament finally accepted O'Connor's plan after much political haggling, the capital was raised in London and preliminary work commenced late in 1892.